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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ), 'gf_id' => 'HOM05D001146', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001146' ), 'data_identifier' => 'HOM05D001146', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001146', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p32120' => 'bna', 'A03p33730' => 'bna', 'A05p11520' => 'bna', 'A05p42910' => 'bna', 'A06p17370' => 'bna', 'A06p38000' => 'bna', 'A07p10880' => 'bna', 'A08p25240' => 'bna', 'A09p04960' => 'bna', 'A09p37130' => 'bna', 'Aa31LG5G15040' => 'aar', 'Aa31LG6G6320' => 'aar', 'Aa31LG9G13970' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.205' => 'aag', 'Actinidia08806' => 'ach', 'Actinidia12138' => 'ach', 'Actinidia13246' => 'ach', 'Actinidia15787' => 'ach', 'Actinidia21997' => 'ach', 'Actinidia22356' => 'ach', 'Actinidia40463' => 'ach', 'Ah.09g226030' => 'amhyb', 'Ah.09g226050' => 'amhyb', 'Ah.10g026770' => 'amhyb', 'Ah.13g066050' => 'amhyb', 'AL1G42950' => 'aly', 'AL3G14660' => 'aly', 'AL4G30060' => 'aly', 'AL6G14820' => 'aly', 'AL7G51300' => 'aly', 'AL864U10010' => 'aly', 'Aqoxy5G00321' => 'aox', 'Aqoxy6G01603' => 'aox', 'Aqoxy7G01784' => 'aox', 'Aqoxy7G02138' => 'aox', 'Aqoxy7G03724' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0BDN0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0H9M9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2R2L9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5FA3RE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8ECF26' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JX7A8U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KW7V4L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2CD11' => 'arhy', 'AT1G29250' => 'ath', 'AT2G34160' => 'ath', 'AT3G04620' => 'ath', 'ATR0322G018' => 'atr', 'ATR0665G131' => 'atr', 'Atru.chr2.857' => 'acertr', 'Atru.chr4.2225' => 'acertr', 'Atru.chr4.2226' => 'acertr', 'Atru.chr7.1218' => 'acertr', 'Atru.chr7.2393' => 'acertr', 'AUR62002249' => 'cqu', 'AUR62011119' => 'cqu', 'AUR62013372' => 'cqu', 'AUR62015460' => 'cqu', 'AUR62024905' => 'cqu', 'AUR62030637' => 'cqu', 'BcaB01g01250' => 'bca', 'BcaB03g12146' => 'bca', 'BcaB03g13897' => 'bca', 'BcaB04g19630' => 'bca', 'BcaB04g21354' => 'bca', 'BcaB06g28739' => 'bca', 'BcaB07g32508' => 'bca', 'BcaC01g00083' => 'bca', 'BcaC01g02502' => 'bca', 'BcaC01g04360' => 'bca', 'BcaC01g05868' => 'bca', 'BcaC02g11472' => 'bca', 'BcaC04g20222' => 'bca', 'BcaC04g23723' => 'bca', 'BcaC05g25232' => 'bca', 'BcaC05g26944' => 'bca', 'BcaC05g26945' => 'bca', 'BcaC05g29920' => 'bca', 'BcaC05g30183' => 'bca', 'BcaC06g35411' => 'bca', 'BcaC08g44644' => 'bca', 'BcaC09g47786' => 'bca', 'BcaNung01725' => 'bca', 'BcaNung02102' => 'bca', 'BcaNung06440' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00940' => 'bna', 'BolC1t05733H' => 'bol', 'BolC2t11137H' => 'bol', 'BolC3t16393H' => 'bol', 'BolC3t19817H' => 'bol', 'BolC4t23073H' => 'bol', 'BolC4t25973H' => 'bol', 'BolC4t26433H' => 'bol', 'BolC5t31518H' => 'bol', 'BolC5t34918H' => 'bol', 'BolC6t38829H' => 'bol', 'BolC6t38903H' => 'bol', 'BolC7t42145H' => 'bol', 'BolC7t42530H' => 'bol', 'BolC7t43312H' => 'bol', 'BolC7t44558H' => 'bol', 'BolC7t46144H' => 'bol', 'BolC9t53463H' => 'bol', 'BolC9t57503H' => 'bol', 'BraA01t03337Z' => 'bra', 'BraA01t04512Z' => 'bra', 'BraA03t12547Z' => 'bra', 'BraA05t20099Z' => 'bra', 'BraA05t22962Z' => 'bra', 'BraA06t24835Z' => 'bra', 'BraA06t26716Z' => 'bra', 'BraA07t28877Z' => 'bra', 'BraA08t33292Z' => 'bra', 'BraA08t34476Z' => 'bra', 'BraA09t36135Z' => 'bra', 'BraA09t39229Z' => 'bra', 'C01p14440' => 'bna', 'C02p44450' => 'bna', 'C02p50590' => 'bna', 'C03p21590' => 'bna', 'C03p41030' => 'bna', 'C03p75600' => 'bna', 'C03p75770' => 'bna', 'C04p14990' => 'bna', 'C04p43920' => 'bna', 'C05p11170' => 'bna', 'C05p27920' => 'bna', 'C05p49770' => 'bna', 'C05p62640' => 'bna', 'C06p19720' => 'bna', 'C06p21600' => 'bna', 'C06p38070' => 'bna', 'C07p16470' => 'bna', 'C07p20090' => 'bna', 'C07p40200' => 'bna', 'C09p03540' => 'bna', 'C09p05350' => 'bna', 'C09p46490' => 'bna', 'CAN.G1230.12' => 'can', 'CAN.G134.64' => 'can', 'CAN.G395.51' => 'can', 'CANSAT11G1857' => 'cansat', 'CANSAT54G1108' => 'cansat', 'CANSAT78G0710' => 'cansat', 'CARHR028520' => 'chi', 'CARHR078830' => 'chi', 'CARHR128250' => 'chi', 'CARHR185250' => 'chi', 'Carub.0001s2740' => 'cru', 'Carub.0003s0378' => 'cru', 'Carub.0004s1579' => 'cru', 'Ca_01067_v3' => 'car', 'Ca_10036_v3' => 'car', 'Ca_20432_v3' => 'car', 'Ca_24425_v3' => 'car', 'Ca_30891_v3' => 'car', 'CBR_g12582' => 'cbr', 'CBR_g6588' => 'cbr', 'Cc02_g30960' => 'ccan', 'Cc03_g04900' => 'ccan', 'Cc04_g04170' => 'ccan', 'Cc06_g08650' => 'ccan', 'Cc08_g00910' => 'ccan', 'CDE02G0434' => 'cde', 'CDE04G1664' => 'cde', 'Cfa003358' => 'cfa', 'Cfa006394' => 'cfa', 'Cfa008376' => 'cfa', 'Cfa013168' => 'cfa', 'Ciclev10009882m.g' => 'ccl', 'Ciclev10009883m.g' => 'ccl', 'Ciclev10026994m.g' => 'ccl', 'Ciclev10030008m.g' => 'ccl', 'Ciclev10030104m.g' => 'ccl', 'CiPaw.01G190100' => 'cil', 'CiPaw.03G243100' => 'cil', 'CiPaw.04G170500' => 'cil', 'CiPaw.08G012400' => 'cil', 'CiPaw.08G121700' => 'cil', 'ClCG02G016810' => 'cla', 'ClCG05G004580' => 'cla', 'ClCG06G010990' => 'cla', 'ClCG11G002950' => 'cla', 'COL.COLO4_03735' => 'col', 'COL.COLO4_05787' => 'col', 'COL.COLO4_15797' => 'col', 'COL.COLO4_23968' => 'col', 'Cpa.g.sc115.7' => 'cpa', 'Cpa.g.sc117.49' => 'cpa', 'Cpa.g.sc117.50' => 'cpa', 'Cpa.g.sc58.51' => 'cpa', 'Cpa.g.sc75.47' => 'cpa', 'Cre09.g401600' => 'cre', 'CsaV3_1G029920' => 'csa', 'CsaV3_2G002770' => 'csa', 'CsaV3_3G012560' => 'csa', 'CSS0005012' => 'camsi', 'CSS0005402' => 'camsi', 'CSS0011952' => 'camsi', 'CSS0024124' => 'camsi', 'CSS0033322' => 'camsi', 'CSS0033728' => 'camsi', 'CSS0040005' => 'camsi', 'CSS0045167' => 'camsi', 'DCAR_000208' => 'dca', 'DCAR_000475' => 'dca', 'DCAR_006223' => 'dca', 'DCAR_006642' => 'dca', 'DCAR_014876' => 'dca', 'DCAR_025323' => 'dca', 'Dinv15961' => 'din', 'Dinv18235' => 'din', 'Dinv20267' => 'din', 'Dinv29907' => 'din', 'Dinv30160' => 'din', 'Dinv30581' => 'din', 'Dinv36536' => 'din', 'Dinv41520' => 'din', 'Dinv44637' => 'din', 'Duzib106G0412' => 'dzi', 'Duzib150G0321' => 'dzi', 'Duzib150G0702' => 'dzi', 'Duzib151G0146' => 'dzi', 'Duzib168G1038' => 'dzi', 'Duzib168G2064' => 'dzi', 'Duzib177G0293' => 'dzi', 'Duzib187G0162' => 'dzi', 'Duzib187G0886' => 'dzi', 'ECA240G4751' => 'eca', 'ECA246G3768' => 'eca', 'ECA247G3975' => 'eca', 'EL10Ac2g02612' => 'bvu', 'EL10Ac3g05889' => 'bvu', 'EL10Ac4g09078' => 'bvu', 'EL10Ac8g18637' => 'bvu', 'Eucgr.C04193' => 'egr', 'Eucgr.F02537' => 'egr', 'Eucgr.H04315' => 'egr', 'FAN02G2151' => 'fan', 'FAN02G3438' => 'fan', 'FAN05G1107' => 'fan', 'FAN05G1692' => 'fan', 'FAN05G1866' => 'fan', 'FAN09G0558' => 'fan', 'FAN09G4194' => 'fan', 'FAN14G3677' => 'fan', 'FAN14G5366' => 'fan', 'FAN14G5635' => 'fan', 'FAN15G3133' => 'fan', 'FAN18G2078' => 'fan', 'FAN20G1388' => 'fan', 'FAN24G2583' => 'fan', 'FAN27G0253' => 'fan', 'FAN27G3493' => 'fan', 'FAN28G0497' => 'fan', 'FvH4_2g29410' => 'fve', 'FvH4_5g27661' => 'fve', 'FvH4_6g02590' => 'fve', 'FvH4_6g30150' => 'fve', 'Glyma.01G234800' => 'gma', 'Glyma.03G248100' => 'gma', 'Glyma.07G031600' => 'gma', 'Glyma.08G211200' => 'gma', 'Glyma.10G163500' => 'gma', 'Glyma.13G364200' => 'gma', 'Glyma.15G009400' => 'gma', 'Glyma.19G246100' => 'gma', 'Glyma.20G226100' => 'gma', 'Gohir.A02G035700' => 'ghi', 'Gohir.A05G009100' => 'ghi', 'Gohir.A05G017200' => 'ghi', 'Gohir.A06G056800' => 'ghi', 'Gohir.A08G236400' => 'ghi', 'Gohir.A11G249900' => 'ghi', 'Gohir.A13G199400' => 'ghi', 'Gohir.D02G042200' => 'ghi', 'Gohir.D03G064700' => 'ghi', 'Gohir.D05G009800' => 'ghi', 'Gohir.D05G018100' => 'ghi', 'Gohir.D06G055200' => 'ghi', 'Gohir.D08G257000' => 'ghi', 'Gohir.D11G260400' => 'ghi', 'Gohir.D13G204900' => 'ghi', 'Gorai.004G274000' => 'gra', 'Gorai.005G046900' => 'gra', 'Gorai.007G278700' => 'gra', 'Gorai.009G010100' => 'gra', 'Gorai.009G018500' => 'gra', 'Gorai.010G064500' => 'gra', 'Gorai.013G105600' => 'gra', 'Gorai.013G233800' => 'gra', 'GSVIVG01015516001' => 'vvi', 'GSVIVG01017289001' => 'vvi', 'GSVIVG01018123001' => 'vvi', 'GSVIVG01018897001' => 'vvi', 'GSVIVG01035831001' => 'vvi', 'HanXRQChr03g0062551' => 'han', 'HanXRQChr04g0096861' => 'han', 'HanXRQChr06g0180281' => 'han', 'HanXRQChr07g0189681' => 'han', 'HanXRQChr12g0368311' => 'han', 'HanXRQChr12g0379731' => 'han', 'HanXRQChr13g0424501' => 'han', 'Haze_11305' => 'cav', 'Haze_21541' => 'cav', 'Haze_25601' => 'cav', 'Hma1.2p1_0000F.1_g000280' => 'hma', 'Hma1.2p1_0650F.1_g195450' => 'hma', 'HPP92_000664' => 'vpl', 'HPP92_000682' => 'vpl', 'HPP92_002793' => 'vpl', 'HPP92_007976' => 'vpl', 'HPP92_023527' => 'vpl', 'HPP92_024116' => 'vpl', 'HPP92_027748' => 'vpl', 'Hund03024' => 'sun', 'Hund09136' => 'sun', 'Hund26501' => 'sun', 'Lalb_Chr06g0168121' => 'lal', 'Lalb_Chr06g0168131' => 'lal', 'Lalb_Chr12g0202531' => 'lal', 'Lalb_Chr14g0373741' => 'lal', 'Lalb_Chr21g0311051' => 'lal', 'Lalb_Chr22g0350941' => 'lal', 'Lalb_Chr24g0395541' => 'lal', 'Lalb_Chr24g0395551' => 'lal', 'Lj3g0012210' => 'lja', 'Lj3g0013174' => 'lja', 'Lj3g0018910' => 'lja', 'Lj4g0013371' => 'lja', 'Lj5g0016076' => 'lja', 'LjContig00222g0017140' => 'lja', 'Lsat_1_v5_gn_3_122761' => 'lsa', 'Lsat_1_v5_gn_5_131341' => 'lsa', 'Lsat_1_v5_gn_5_37441' => 'lsa', 'Lsat_1_v5_gn_7_45641' => 'lsa', 'Manes.03G016400' => 'mes', 'Manes.08G136600' => 'mes', 'Manes.09G151000' => 'mes', 'Manes.16G120500' => 'mes', 'Mapoly0045s0036' => 'mpo', 'MBI01_g37802_MAGBIO' => 'mbi', 'MBI04_g07647_MAGBIO' => 'mbi', 'MBI04_g08002_MAGBIO' => 'mbi', 'MBI04_g38142_MAGBIO' => 'mbi', 'MBI07_g27648_MAGBIO' => 'mbi', 'MBI07_g30191_MAGBIO' => 'mbi', 'MBI11_g34853_MAGBIO' => 'mbi', 'MBI19_g17775_MAGBIO' => 'mbi', 'MCO05G076' => 'mco', 'MD04G1226900' => 'mdo', 'MD08G1147300' => 'mdo', 'MD08G1188700' => 'mdo', 'MD09G1220100' => 'mdo', 'MD12G1243900' => 'mdo', 'MD15G1123300' => 'mdo', 'MD15G1378600' => 'mdo', 'MD16G1209300' => 'mdo', 'MD17G1207900' => 'mdo', 'Medtr1g080680' => 'mtr', 'Medtr2g103500' => 'mtr', 'Medtr4g011000' => 'mtr', 'Medtr5g006970' => 'mtr', 'MELO3C004397.2' => 'cme', 'MELO3C004516.2' => 'cme', 'MELO3C006467.2' => 'cme', 'MELO3C010358.2' => 'cme', 'Migut.D01061' => 'egut', 'Migut.K00476' => 'egut', 'Migut.N01921' => 'egut', 'MSTRG.20463' => 'ama', 'MSTRG.25999' => 'ama', 'MSTRG.4714' => 'ama', 'MSTRG.9435' => 'ama', 'Nitab4.5_0000109g0230' => 'nta', 'Nitab4.5_0000268g0030' => 'nta', 'Nitab4.5_0000447g0050' => 'nta', 'Nitab4.5_0001910g0010' => 'nta', 'Nitab4.5_0002247g0140' => 'nta', 'Nitab4.5_0005761g0040' => 'nta', 'Nitab4.5_0011211g0030' => 'nta', 'Nn2g12008' => 'nnu', 'Nn3g19544' => 'nnu', 'Nn8g39418' => 'nnu', 'Oeu008543.1' => 'oeu', 'Oeu016450.1' => 'oeu', 'Oeu018463.1' => 'oeu', 'Oeu033471.1' => 'oeu', 'Oeu036564.1' => 'oeu', 'Oeu038467.1' => 'oeu', 'Oeu047074.1' => 'oeu', 'Oeu058084.1' => 'oeu', 'Os01g0173100' => 'osa', 'Os02g0202500' => 'osa', 'Os06g0602600' => 'osa', 'Os12g0489300' => 'osa', 'Peaxi162Scf00073g01110' => 'pax', 'Peaxi162Scf00148g00154' => 'pax', 'Peaxi162Scf00207g00735' => 'pax', 'Peaxi162Scf00643g00432' => 'pax', 'Peaxi162Scf00647g00117' => 'pax', 'PGR004G0972' => 'pgr', 'PGR102G3015' => 'pgr', 'PGR102G3033' => 'pgr', 'PGR142G1677' => 'pgr', 'PGSC0003DMG400020460' => 'stu', 'PGSC0003DMG400020480' => 'stu', 'PGSC0003DMG400027494' => 'stu', 'PGSC0003DMG400028540' => 'stu', 'Phvul.002G042200' => 'pvu', 'Phvul.005G176200' => 'pvu', 'Phvul.006G103000' => 'pvu', 'Phvul.007G188600' => 'pvu', 'Phvul.010G154500' => 'pvu', 'Potri.005G056000' => 'ptr', 'Potri.006G252000' => 'ptr', 'Potri.013G042900' => 'ptr', 'Potri.018G029300' => 'ptr', 'Pp3c12_20320' => 'ppa', 'Pp3c12_20750' => 'ppa', 'Pp3c12_20960' => 'ppa', 'Pp3c12_21020' => 'ppa', 'PRCOL_00003661' => 'pco', 'Prupe.1G031300' => 'ppe', 'Prupe.1G478700' => 'ppe', 'Prupe.3G082200' => 'ppe', 'Prupe.6G345600' => 'ppe', 'Psat2g189840' => 'psa', 'Psat5g301560' => 'psa', 'Psat6g145520' => 'psa', 'Psat7g256120' => 'psa', 'Psat7g256200' => 'psa', 'PSO170G3706' => 'pso', 'PSO210G3388' => 'pso', 'PSO210G3860' => 'pso', 'PSO210G6383' => 'pso', 'PSO210G7291' => 'pso', 'PSO455G0008' => 'pso', 'QL02p022233' => 'qlo', 'QL02p088069' => 'qlo', 'QL03p027772' => 'qlo', 'RcHm_v2.0_Chr2g0136361' => 'rch', 'RcHm_v2.0_Chr3g0450501' => 'rch', 'RcHm_v2.0_Chr6g0298211' => 'rch', 'Rhsim01G0074300' => 'rsi', 'Rhsim02G0033300' => 'rsi', 'Rhsim07G0074800' => 'rsi', 'Sabra06G0197000' => 'sbr', 'Sabra13G0039400' => 'sbr', 'Sabra18G0031400' => 'sbr', 'SalBow1G3588' => 'sbo', 'SalBow2G0655' => 'sbo', 'Sc06g0000630' => 'sci', 'Sc09g0004040' => 'sci', 'Sc18g0000650' => 'sci', 'Sc25g0004130' => 'sci', 'Sed0001424' => 'sed', 'Sed0003756' => 'sed', 'Sed0004268' => 'sed', 'Sed0005227' => 'sed', 'Sed0006160' => 'sed', 'Sed0017001' => 'sed', 'Sed0018671' => 'sed', 'SEGI_07972' => 'sgi', 'SEGI_11011' => 'sgi', 'SEGI_22999' => 'sgi', 'SGA_v2.0_scaffold117G32359' => 'sas', 'SGA_v2.0_scaffold16G07606' => 'sas', 'SGA_v2.0_scaffold172G38979' => 'sas', 'SGA_v2.0_scaffold196G40969' => 'sas', 'SGA_v2.0_scaffold229G43322' => 'sas', 'SGA_v2.0_scaffold45G17073' => 'sas', 'SHI41753' => 'shi', 'SMO347G0643' => 'smo', 'SMO361G0320' => 'smo', 'Solyc06g065980.3' => 'sly', 'Solyc06g066100.3' => 'sly', 'Solyc06g068050.3' => 'sly', 'Sopen01g040740' => 'spe', 'Sopen06g024460' => 'spe', 'Sopen06g024580' => 'spe', 'Sopen06g025330' => 'spe', 'Sp1g25130' => 'spa', 'Sp2g20120' => 'spa', 'Sp3g03470' => 'spa', 'Sp4g16470' => 'spa', 'Sp7g30190' => 'spa', 'TAR365G0090' => 'tar', 'TAR383G0930' => 'tar', 'TAR625G0892' => 'tar', 'TAR626G1425' => 'tar', 'TAR636G1505' => 'tar', 'TAR636G1933' => 'tar', 'THA.LOC104799257' => 'tha', 'THA.LOC104803669' => 'tha', 'THA.LOC104803833' => 'tha', 'THA.LOC104812640' => 'tha', 'THA.LOC104815141' => 'tha', 'THA.LOC104820598' => 'tha', 'THA.LOC104821665' => 'tha', 'Thecc.04G246500' => 'tca', 'Thecc.05G280300' => 'tca', 'Thecc.09G124600' => 'tca', 'Thecc.09G150600' => 'tca', 'Thhalv10005588m.g' => 'esa', 'Thhalv10009096m.g' => 'esa', 'Thhalv10017416m.g' => 'esa', 'Thhalv10021676m.g' => 'esa', 'TPR.G21819' => 'tpr', 'TPR.G27501' => 'tpr', 'TPR.G36329' => 'tpr', 'TPR.G37294' => 'tpr', 'TPR.G37916' => 'tpr', 'TWI09G0565' => 'twi', 'TWI32G0412' => 'twi', 'TWI32G0609' => 'twi', 'TWI34G0585' => 'twi', 'TWI53G1783' => 'twi', 'TWI53G1908' => 'twi', 'TWI63G1454' => 'twi', 'unitig_699.g19241' => 'ugi', 'unitig_699.g19824' => 'ugi', 'unitig_747.g21295' => 'ugi', 'unitig_748.g7148' => 'ugi', 'vmacro13818' => 'vma', 'vmacro15409' => 'vma', 'vmacro16907' => 'vma', 'vmacro20544' => 'vma', 'VMungo0331G1523' => 'vmu', 'VMungo0540G0382' => 'vmu', 'VMungo0540G0934' => 'vmu', 'VMungo0720G1366' => 'vmu', 'VMungo1080G0376' => 'vmu', 'VMungo1215G1705' => 'vmu', 'VMungo1215G2522' => 'vmu', 'Zm00001eb122780' => 'zma', 'Zm00001eb122810' => 'zma', 'Zm00001eb205590' => 'zma', 'Zm00001eb336800' => 'zma', 'Zm00001eb345760' => 'zma', 'Zm00001eb408660' => 'zma' ) $gf_id = 'HOM05D001146' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001146' ) $data_identifier = 'HOM05D001146' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 33, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 8, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 25, 'bol' => (int) 18, 'bra' => (int) 12, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 4, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 8, 'dca' => (int) 6, 'din' => (int) 9, 'dzi' => (int) 9, 'eca' => (int) 3, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 17, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 15, 'gra' => (int) 8, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 3, 'lal' => (int) 8, 'lja' => (int) 6, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 8, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb408660' $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